Update adapters and converters #243
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| name: Test and Deploy bioimageio.core | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ "**" ] | |
| defaults: | |
| run: | |
| shell: micromamba-shell {0} | |
| jobs: | |
| black: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: psf/black@stable | |
| with: | |
| options: "--check" | |
| src: "." | |
| jupyter: true | |
| version: "24.3" | |
| test-spec-conda: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.9', '3.10', '3.11', '3.12'] | |
| include: | |
| - python-version: '3.12' | |
| run-expensive-tests: true | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install Conda environment with Micromamba | |
| if: matrix.python-version != '3.8' | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| cache-downloads: true | |
| cache-environment: true | |
| environment-file: dev/env-wo-python.yaml | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| post-cleanup: 'all' | |
| - name: Install py3.8 environment | |
| if: matrix.python-version == '3.8' | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| cache-downloads: true | |
| cache-environment: true | |
| environment-file: dev/env-py38.yaml | |
| post-cleanup: 'all' | |
| - name: additional setup | |
| run: pip install --no-deps -e . | |
| - name: Get Date | |
| id: get-date | |
| run: | | |
| echo "date=$(date +'%Y-%b')" | |
| echo "date=$(date +'%Y-%b')" >> $GITHUB_OUTPUT | |
| shell: bash | |
| - uses: actions/cache@v4 | |
| with: | |
| path: bioimageio_cache | |
| key: "test-spec-conda-${{ steps.get-date.outputs.date }}" | |
| - name: pytest-spec-conda | |
| run: pytest --disable-pytest-warnings | |
| env: | |
| BIOIMAGEIO_CACHE_PATH: bioimageio_cache | |
| RUN_EXPENSIVE_TESTS: ${{ matrix.run-expensive-tests && 'true' || 'false' }} | |
| test-spec-main: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.12'] | |
| include: | |
| - python-version: '3.12' | |
| report-coverage: true | |
| run-expensive-tests: true | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install Conda environment with Micromamba | |
| if: matrix.python-version != '3.8' | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| cache-downloads: true | |
| cache-environment: true | |
| environment-file: dev/env-wo-python.yaml | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| post-cleanup: 'all' | |
| - name: Install py3.8 environment | |
| if: matrix.python-version == '3.8' | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| cache-downloads: true | |
| cache-environment: true | |
| environment-file: dev/env-py38.yaml | |
| post-cleanup: 'all' | |
| - name: additional setup spec | |
| run: | | |
| conda remove --yes --force bioimageio.spec || true # allow failure for cached env | |
| pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io | |
| - name: additional setup core | |
| run: pip install --no-deps -e . | |
| - name: Get Date | |
| id: get-date | |
| run: | | |
| echo "date=$(date +'%Y-%b')" | |
| echo "date=$(date +'%Y-%b')" >> $GITHUB_OUTPUT | |
| shell: bash | |
| - uses: actions/cache@v4 | |
| with: | |
| path: bioimageio_cache | |
| key: "test-spec-main-${{ steps.get-date.outputs.date }}" | |
| - name: pytest-spec-main | |
| run: pytest --disable-pytest-warnings | |
| env: | |
| BIOIMAGEIO_CACHE_PATH: bioimageio_cache | |
| RUN_EXPENSIVE_TESTS: ${{ matrix.run-expensive-tests && 'true' || 'false' }} | |
| - if: matrix.report-coverage && github.event_name == 'pull_request' | |
| uses: orgoro/[email protected] | |
| with: | |
| coverageFile: coverage.xml | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - if: matrix.report-coverage && github.ref == 'refs/heads/main' | |
| run: | | |
| pip install genbadge[coverage] | |
| genbadge coverage --input-file coverage.xml --output-file ./dist/coverage/coverage-badge.svg | |
| coverage html -d dist/coverage | |
| - if: matrix.report-coverage && github.ref == 'refs/heads/main' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage | |
| retention-days: 1 | |
| path: dist | |
| test-spec-main-tf: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.9', '3.12'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| cache-downloads: true | |
| cache-environment: true | |
| environment-file: dev/env-tf.yaml | |
| condarc: | | |
| channel-priority: flexible | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| post-cleanup: 'all' | |
| - name: additional setup spec | |
| run: | | |
| conda remove --yes --force bioimageio.spec || true # allow failure for cached env | |
| pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io | |
| - name: additional setup core | |
| run: pip install --no-deps -e . | |
| - name: Get Date | |
| id: get-date | |
| run: | | |
| echo "date=$(date +'%Y-%b')" | |
| echo "date=$(date +'%Y-%b')" >> $GITHUB_OUTPUT | |
| shell: bash | |
| - uses: actions/cache@v4 | |
| with: | |
| path: bioimageio_cache | |
| key: "test-spec-main-tf-${{ steps.get-date.outputs.date }}" | |
| - run: pytest --disable-pytest-warnings | |
| env: | |
| BIOIMAGEIO_CACHE_PATH: bioimageio_cache | |
| test-spec-conda-tf: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.9', '3.12'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| cache-downloads: true | |
| cache-environment: true | |
| environment-file: dev/env-tf.yaml | |
| condarc: | | |
| channel-priority: flexible | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| post-cleanup: 'all' | |
| - name: additional setup | |
| run: pip install --no-deps -e . | |
| - name: Get Date | |
| id: get-date | |
| run: | | |
| echo "date=$(date +'%Y-%b')" | |
| echo "date=$(date +'%Y-%b')" >> $GITHUB_OUTPUT | |
| shell: bash | |
| - uses: actions/cache@v4 | |
| with: | |
| path: bioimageio_cache | |
| key: "test-spec-conda-tf-${{ steps.get-date.outputs.date }}" | |
| - name: pytest-spec-tf | |
| run: pytest --disable-pytest-warnings | |
| env: | |
| BIOIMAGEIO_CACHE_PATH: bioimageio_cache | |
| conda-build: | |
| runs-on: ubuntu-latest | |
| needs: test-spec-conda | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Install Conda environment with Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| cache-downloads: true | |
| cache-environment: true | |
| environment-name: build-env | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| create-args: | | |
| boa | |
| - name: linux conda build | |
| run: | | |
| conda mambabuild -c conda-forge conda-recipe | |
| docs: | |
| needs: [test-spec-main] | |
| if: github.ref == 'refs/heads/main' | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: coverage | |
| path: dist | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| cache: 'pip' | |
| - run: pip install -e .[dev] | |
| - name: Generate developer docs | |
| run: ./scripts/pdoc/run.sh | |
| - run: cp README.md ./dist/README.md | |
| - name: copy rendered presentations | |
| run: | | |
| mkdir ./dist/presentations | |
| cp -r ./presentations/*.html ./dist/presentations/ | |
| - name: Deploy to gh-pages 🚀 | |
| uses: JamesIves/github-pages-deploy-action@v4 | |
| with: | |
| branch: gh-pages | |
| folder: dist |